Contacts of the helix formed by residues 1551 - 1559 (chain A) in PDB entry 3PT6
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER1551 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1380A ILE* 4.0 6.7 - - - -
1415A HIS* 2.8 34.4 + - - -
1416A ILE 3.3 25.1 - - - -
1417A CYS* 4.2 1.3 - - - -
1548A ARG* 3.6 2.8 - - - +
1550A VAL* 1.3 76.3 - - - +
1552A VAL* 1.3 64.4 + - - +
1553A ARG 3.7 1.0 + - - -
1554A GLU* 2.6 37.7 + - - +
1555A CYS* 3.1 20.4 + - - -
1575A HIS* 3.8 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1552 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1414A ASP* 3.5 22.2 + - + +
1416A ILE* 3.1 21.6 + - + +
1551A SER* 1.3 71.8 - - - +
1553A ARG* 1.3 56.7 + - - +
1555A CYS* 3.3 3.8 + - - +
1556A ALA* 2.9 25.1 + - - +
1567A PHE* 4.6 7.0 - - + -
1571A ILE* 3.8 17.0 - - + +
1574A ARG* 3.9 23.1 - - + -
1575A HIS* 3.4 36.1 - - + +
1578A VAL* 4.3 16.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1553 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1377A LEU* 4.4 9.4 - - + -
1412A LEU* 3.7 20.4 - - + -
1413A ARG* 2.9 36.0 + - - +
1414A ASP* 3.0 29.1 + - - +
1415A HIS* 4.3 7.2 - - - +
1551A SER* 3.2 5.4 - - - +
1552A VAL* 1.3 72.7 - - - +
1554A GLU* 1.3 55.7 + - - +
1555A CYS 3.0 1.6 - - - -
1556A ALA* 2.9 12.3 + - - +
1557A ARG* 2.6 52.1 + - + +
1561A PHE* 4.8 1.2 + - - +
1562A PRO 3.9 5.1 + - - -
1563A ASP* 3.7 44.2 + - - +
1565A TYR 3.5 21.6 + - - -
1567A PHE* 3.6 20.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1554 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1373A THR* 4.3 1.0 - - - +
1374A MET* 4.0 24.1 - - + +
1377A LEU* 3.5 20.2 - - + +
1415A HIS* 4.0 3.0 - - - -
1525A PHE* 3.8 7.4 - - - -
1543A HIS* 3.0 29.2 + - - -
1548A ARG* 2.6 31.6 + - - -
1550A VAL* 3.2 14.5 - - + +
1551A SER* 2.6 37.6 + - - +
1553A ARG* 1.3 75.6 - - - +
1555A CYS* 1.3 58.8 + - - +
1557A ARG* 3.4 9.3 + - - +
1558A SER* 3.0 25.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1555 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1525A PHE* 4.9 4.9 - - - -
1528A THR* 4.1 17.9 - - + -
1529A VAL* 4.9 6.7 - - - -
1532A PRO* 5.0 3.4 - - - -
1550A VAL* 3.8 28.0 - - - -
1551A SER 3.1 11.2 + - - +
1552A VAL 3.5 8.1 - - - +
1553A ARG 3.0 0.6 - - - -
1554A GLU* 1.3 73.2 - - - +
1556A ALA* 1.3 67.4 + - - +
1557A ARG 2.9 1.6 - - - -
1558A SER* 2.7 26.0 + - - -
1559A GLN* 3.0 9.2 + - - +
1575A HIS* 4.0 20.6 - - - +
1578A VAL* 3.6 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1556 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1552A VAL 2.9 15.0 + - - +
1553A ARG* 3.4 22.0 - - - +
1555A CYS* 1.3 76.2 - - - +
1557A ARG* 1.3 60.0 + - - +
1559A GLN 3.3 6.8 - - - +
1561A PHE* 3.2 34.7 + - + +
1567A PHE* 3.7 33.9 - - + -
1578A VAL* 3.5 14.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1557 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1373A THR* 2.8 37.4 + - + +
1374A MET* 3.7 3.3 - - + +
1376A ASP* 2.8 39.8 + - - -
1377A LEU* 3.4 19.6 - - + +
1391A TYR* 4.1 2.2 - - - -
1399A PHE* 3.4 21.4 - - - -
1400A GLN* 4.0 7.8 - - - +
1403A LEU* 3.7 26.8 - - - +
1404A ARG* 3.8 10.7 - - - +
1412A LEU* 5.3 0.4 - - - +
1553A ARG* 2.6 33.5 + - + +
1554A GLU* 3.4 9.4 - - - +
1556A ALA* 1.3 71.1 - - - +
1558A SER* 1.3 57.7 + - - +
1559A GLN 2.7 16.5 - - - +
1561A PHE 5.0 0.9 - - - +
1563A ASP* 2.8 38.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1558 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1309A VAL* 3.0 28.4 - - - +
1310A ALA 4.2 3.2 + - - +
1311A GLN* 3.3 7.1 - - - +
1373A THR* 4.4 7.6 - - - -
1525A PHE* 3.5 40.0 - - - -
1528A THR* 2.5 26.4 + - - -
1554A GLU 3.0 11.1 + - - -
1555A CYS* 2.7 20.2 + - - -
1557A ARG* 1.3 71.8 - - - +
1559A GLN* 1.3 61.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1559 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1309A VAL* 3.6 10.0 - - - +
1311A GLN* 3.0 22.6 + - - +
1313A ARG* 3.5 16.5 - - - +
1399A PHE* 4.3 1.0 - - - -
1403A LEU* 5.3 0.2 - - - +
1528A THR* 4.0 8.4 - - - +
1555A CYS 3.0 10.5 + - - +
1556A ALA 3.3 11.8 - - - +
1557A ARG 2.7 20.8 - - - +
1558A SER* 1.3 78.2 + - - +
1560A GLY* 1.3 60.4 + - - +
1561A PHE* 3.7 13.2 - - + -
1578A VAL* 2.7 37.1 + - + +
1579A GLY* 3.6 6.7 + - - -
1581A ALA 3.3 16.7 + - - -
1583A PRO* 3.1 25.3 - - + +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il